Review: Assessing available genetic diversity estimates of rare breeds of livestock

Abstract

11 The United Kingdom (UK) is home to many local and rare livestock breeds. The local 12 breed populations are highly adapted to specific environments in the UK and these 13 and other rare breeds provide solutions to niche needs. Rare breeds often contribute 14 more than expected to overall species genetic diversity, which is important because 15 genetic variation is needed for adapting to new challenges. It is therefore very 16 important from both UK and global perspectives to maintain genetic diversity of rare 17 livestock breeds in the UK, and to do this, we need to evaluate the monitoring of 18 genetic diversity to identify gaps in our knowledge and prioritise resources reserved 19 for conservation purposes. The objectives of this study were to survey the literature 20 to: (1) summarise genetic/genomic characterisation (effective population size (Ne) 21 and inbreeding) of domestic populations (livestock and equine) in the UK and Ireland; 22 (2) compare number of populations on the UK’s Rare Breed Survival Trust (RBST) 23 watch list and the number of UK and Irish populations in the peer-reviewed literature 24 with inbreeding, genetic diversity and/or Ne estimates; and (3) compare annually bioRxiv preprint doi: https://doi.org/10.1101/2025.05.14.653764; this version posted May 17, 2025. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. 25 reported (census-based) estimates of Ne with (inbreeding and DNA-based) estimates 26 from peer-reviewed literature. We found a total of 37 publications with Ne or 27 inbreeding estimates for UK or Ireland livestock populations, published from 1975 to 28 2024. While many (42%) of the breeds on the RBST watchlist have been included in 29 publications, there are still many breeds, and a few species (turkey, duck and geese) 30 with no publicly available pedigree- or DNA-based genetic diversity measures. We 31 found census-based Ne estimates were, on average, higher than DNA-based 32 estimates, likely due to violated assumptions when estimating Ne with census-based 33 data because of the way livestock mating systems are designed. Most peer-reviewed 34 papers estimated genetic diversity measures using pedigree, microsatellite markers, 35 or SNP markers. To identify breed-unique variants responsible for adaptive traits in 36 rare breeds, more studies using whole-genome sequencing will be needed. 37 Altogether, we have summarised the genetic diversity estimates on UK livestock 38 populations, identifying gaps in knowledge. 39 40 Keywords: Genetic diversity, inbreeding, effective population size (Ne), rare breeds, 41 livestock, equine 42 43 Implications 44 Maintaining genetic diversity in livestock helps safeguard against future challenges to 45 our food production systems. We surveyed publicly available measures of genetic 46 diversity for farm animal populations in the UK (including government, Rare Breed 47 Survival Trust (RBST), and peer-reviewed scientific publications) to identify any gaps. 48 We found census-based estimates of genetic diversity, which are used to inform and bioRxiv preprint doi: https://doi.org/10.1101/2025.05.14.653764; this version posted May 17, 2025. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. 49 prioritise resources for conservation efforts, on average, are likely overestimating 50 available genetic diversity. Additionally, most farm animal breeds had only these 51 census-based estimates. Genetic diversity estimates could be improved using 52 pedigree or DNA information, more accurately identifying endangered breeds. 53 54